Mercurial > repos > dereeper > sniplay
comparison AnnotationStatsFromVCF/annotationStatsFromVCF_wrapper.xml @ 9:98c37a5d67f4 draft
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author | dereeper |
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date | Wed, 07 Feb 2018 22:08:47 -0500 |
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children | c6640c49fd01 |
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8:6bf69b40365c | 9:98c37a5d67f4 |
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1 <tool id="annotationStatsFromVCF" name="Get annotation statistics" version="1.0.0"> | |
2 <description> from VCF file </description> | |
3 <requirements> | |
4 <requirement type="binary">perl</requirement> | |
5 <requirement type="package" version="0.1.12b">vcftools</requirement> | |
6 </requirements> | |
7 <stdio> | |
8 <exit_code range="1:" /> | |
9 </stdio> | |
10 <command interpreter="perl"> | |
11 AnnotationStatsFromVCF.pl -v $input -o $output_label -s $step && mv ${output_label} $output_count && mv ${output_label}.effect $output_stats_effect && mv ${output_label}.location $output_stats_location | |
12 </command> | |
13 <inputs> | |
14 <param type="data" name="input" format="vcf" label="VCF file" /> | |
15 <param type="text" name="output_label" label="Output_label" value='VCF_stats' /> | |
16 </inputs> | |
17 <outputs> | |
18 <data name="output_count" format="txt" label="${output_label}."/> | |
19 <data name="output_stats_effect" format="txt" label="${output_label}."/> | |
20 <data name="output_stats_location" format="txt" label="${output_label}."/> | |
21 </outputs> | |
22 <tests> | |
23 <test> | |
24 <param name="input" value="vcf2fastaAndHapmap-sample.vcf"/> | |
25 <output name="output_count" file="vcf2fastaAndHapmap-sample.vcf"/> | |
26 <output name="output_stats_effect" file="vcf2fastaAndHapmap-sample.vcf"/> | |
27 <output name="output_stats_location" file="vcf2fastaAndHapmap-sample.vcf"/> | |
28 </test> | |
29 </tests> | |
30 <help><![CDATA[ | |
31 | |
32 .. class:: infomark | |
33 | |
34 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform | |
35 | |
36 | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). | |
37 | |
38 .. class:: infomark | |
39 | |
40 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. | |
41 | |
42 .. class:: infomark | |
43 | |
44 **Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr | |
45 | |
46 --------------------------------------------------- | |
47 | |
48 ============================== | |
49 Get Haplotypes From Phased VCF | |
50 ============================== | |
51 | |
52 ----------- | |
53 Description | |
54 ----------- | |
55 | |
56 | Get Haplotype from phased VCF | |
57 | |
58 ----------------- | |
59 Workflow position | |
60 ----------------- | |
61 | |
62 **Upstream tool** | |
63 | |
64 =============== ========================== ======= | |
65 Name output file(s) format | |
66 =============== ========================== ======= | |
67 Beagle Phased VCF file VCF | |
68 =============== ========================== ======= | |
69 | |
70 | |
71 **Downstream tool** | |
72 | |
73 =============== ========================== =========== | |
74 Name input file(s) format | |
75 =============== ========================== =========== | |
76 =============== ========================== =========== | |
77 | |
78 | |
79 ---------- | |
80 Input file | |
81 ---------- | |
82 | |
83 VCF file | |
84 Phased VCF file | |
85 | |
86 ---------- | |
87 Parameters | |
88 ---------- | |
89 | |
90 Output file basename | |
91 Prefix for the output VCF file | |
92 | |
93 ------------ | |
94 Output files | |
95 ------------ | |
96 | |
97 | |
98 Text file | |
99 File describing haplotypes | |
100 | |
101 Fasta file | |
102 Fasta file with haplotypes | |
103 | |
104 --------------------------------------------------- | |
105 | |
106 --------------- | |
107 Working example | |
108 --------------- | |
109 | |
110 Input files | |
111 =========== | |
112 | |
113 VCF file | |
114 --------- | |
115 | |
116 :: | |
117 | |
118 #fileformat=VCFv4.1 | |
119 #FILTER=<ID=LowQual,Description="Low quality"> | |
120 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | |
121 [...] | |
122 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AZUCENA | |
123 Chr1 4299 . G A . PASS AR2=1;DR2=1;AF=0.168 GT:DS:GP 0|0:0:1,0,0 | |
124 | |
125 | |
126 Parameters | |
127 ========== | |
128 | |
129 Output name -> haplotypes | |
130 | |
131 | |
132 Output files | |
133 ============ | |
134 | |
135 haplotypes.distinct_haplotypes.txt | |
136 ---------------------------------- | |
137 | |
138 :: | |
139 | |
140 ===Chr10=== | |
141 haplo1:2:CIRAD403_1,CIRAD403_2, | |
142 TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT | |
143 haplo2:2:MAHAE_1,MAHAE_2, | |
144 TAAATCTTGGTGCTGATCTGATATTTAATGCGT | |
145 | |
146 | |
147 haplotypes.haplo.fas | |
148 -------------------- | |
149 | |
150 :: | |
151 | |
152 >Chr10_AZUCENA_1 | |
153 TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT | |
154 >Chr10_AZUCENA_2 | |
155 TAAATCTTGGTGCTGATCTGATATTTAATGCGT | |
156 | |
157 ]]></help> | |
158 <citations> | |
159 <!-- [HELP] As DOI or BibTex entry --> | |
160 <citation type="bibtex">@article{Dereeper03062015, | |
161 author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, | |
162 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, | |
163 year = {2015}, | |
164 doi = {10.1093/nar/gkv351}, | |
165 abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, | |
166 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, | |
167 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, | |
168 journal = {Nucleic Acids Research} | |
169 } | |
170 | |
171 }</citation> | |
172 | |
173 </citations> | |
174 | |
175 </tool> |